Analysis of mutagenesis by APOBEC cytidine deaminases (P-MACD).
View Report | There are 236 tumor samples in this analysis. The Benjamini-Hochberg-corrected p-value for enrichment of the APOBEC mutation signature in 6 samples is <=0.05. Out of these, 2 have enrichment values >2, which implies that in such samples at least 50% of APOBEC signature mutations have been in fact made by APOBEC enzyme(s).

Mutation Assessor
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Mutation Signature Analysis
View Report | Our analysis idenfied 1 solution(s) of mutational signatures across 236 samples by BayesNMF method.

SNP6 Copy number analysis (GISTIC2)
View Report | There were 260 tumor samples used in this analysis: 36 significant arm-level results, 24 significant focal amplifications, and 36 significant focal deletions were found.

Correlation between aggregated molecular cancer subtypes and selected clinical features
View Report | Testing the association between subtypes identified by 10 different clustering approaches and 9 clinical features across 261 patients, 59 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between APOBEC groups and selected clinical features
View Report | Testing the association between APOBEC groups identified by 2 different apobec score and 9 clinical features across 236 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.

Correlation between APOBEC signature variables and clinical features
View Report | Testing the association between 3 variables and 9 clinical features across 236 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one variables.

Correlation between copy number variation genes (focal events) and selected clinical features
View Report | Testing the association between copy number variation 60 focal events and 9 clinical features across 260 patients, 174 significant findings detected with Q value < 0.25.

Correlation between copy number variations of arm-level result and selected clinical features
View Report | Testing the association between copy number variation 82 arm-level events and 9 clinical features across 260 patients, 61 significant findings detected with Q value < 0.25.

Correlation between gene mutation status and selected clinical features
View Report | Testing the association between mutation status of 5 genes and 9 clinical features across 236 patients, 8 significant findings detected with Q value < 0.25.

Correlation between mutation rate and clinical features
View Report | Testing the association between 2 variables and 10 clinical features across 236 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one variables.

Clustering of copy number data by focal peak region with absolute value: consensus NMF
View Report | The most robust consensus NMF clustering of 260 samples using the 60 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of copy number data by peak region with threshold value: consensus NMF
View Report | The most robust consensus NMF clustering of 260 samples using the 60 most variable genes was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of lincRNA expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 2500 most variable lincRNAs. Consensus ward linkage hierarchical clustering of 258 samples and 2500 lincRNAs identified 5 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of lincRNA expression: consensus NMF
View Report | The most robust consensus NMF clustering of 259 samples using the 2500 most variable lincRNAs was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of miR mature expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 273 most variable miRs. Consensus ward linkage hierarchical clustering of 258 samples and 273 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Clustering of miR mature expression: consensus NMF
View Report | The most robust consensus NMF clustering of 259 samples using the 273 most variable miRs was identified for k = 4 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of protein coding gene expression: consensus NMF
View Report | The most robust consensus NMF clustering of 259 samples using the 2500 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Clustering of Protein-coding gene expression: consensus hierarchical
View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 258 samples and 2500 genes identified 6 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Identification of putative miR direct targets by sequencing data
View Report | The CLR algorithm was applied on 766 miRs and 18776 mRNAs across 257 samples. After 2 filtering steps, the number of 129 miR:gene pairs were detected.

Methylation__HM450_Clustering_CNMF
View Report | The most robust consensus NMF clustering of 261 samples using the 17546 most variable genes was identified for k = 7 clusters. We computed the clustering for k = 2 to k = 10 and used the cophenetic correlation coefficient and the average silhouette width calculation to determine the robust clusters.

Methylation__HM450_Clustering_Consensus_Plus
View Report | Median absolute deviation (MAD) was used to select 2500 most variable genes. Consensus ward linkage hierarchical clustering of 260 samples and 2500 genes identified 4 subtypes with the stability of the clustering increasing for k = 2 to k = 10.

Mutation_MutSig2CV
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Correlation between copy number variation genes (focal events) and molecular subtypes
View Report | Testing the association between copy number variation 60 focal events and 10 molecular subtypes across 260 patients, 444 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between copy number variations of arm-level result and molecular subtypes
View Report | Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 260 patients, 390 significant findings detected with P value < 0.05 and Q value < 0.25.

Correlation between gene mutation status and molecular subtypes
View Report | Testing the association between mutation status of 5 genes and 10 molecular subtypes across 236 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.